Sea slug has taken genes from algae it eats, allowing it to photosynthesize like a plant

February 3, 2015 by Diana Kenney
The rich green color of the photosynthesizing sea slug, Elysia chlorotica, helps to camouflage it on the ocean floor. Credit: Patrick Krug

How a brilliant-green sea slug manages to live for months at a time "feeding" on sunlight, like a plant, is clarified in a recent study published in The Biological Bulletin.

The authors present the first direct evidence that the emerald green sea slug's chromosomes have some that come from the algae it eats.

These genes help sustain photosynthetic processes inside the slug that provide it with all the food it needs.

Importantly, this is one of the only known examples of functional gene transfer from one multicellular species to another, which is the goal of to correct genetically based diseases in humans.

"Is a a good [biological model] for a human therapy? Probably not. But figuring out the mechanism of this naturally occurring gene transfer could be extremely instructive for future medical applications," says study co-author Sidney K. Pierce, an emeritus professor at University of South Florida and at University of Maryland, College Park.

The team used an advanced imaging technique to confirm that a gene from the alga V. litorea is present on the E. chlorotica slug's chromosome. This gene makes an enzyme that is critical to the function of photosynthetic "machines" called , which are typically found in plants and algae.

It has been known since the 1970s that E. chloritica "steals" chloroplasts from V. litorea (called "kleptoplasty") and embeds them into its own digestive cells. Once inside the slug cells, the chloroplasts continue to photosynthesize for up to nine months—much longer than they would perform in the algae. The photosynthesis process produces carbohydrates and lipids, which nourish the slug.

How the slug manages to maintain these photosynthesizing organelles for so long has been the topic of intensive study and a good deal of controversy. "This paper confirms that one of several algal genes needed to repair damage to chloroplasts, and keep them functioning, is present on the slug chromosome," Pierce says. "The gene is incorporated into the slug chromosome and transmitted to the next generation of slugs." While the next generation must take up chloroplasts anew from algae, the genes to maintain the chloroplasts are already present in the slug genome, Pierce says.

"There is no way on earth that genes from an alga should work inside an animal cell," Pierce says. "And yet here, they do. They allow the animal to rely on sunshine for its nutrition. So if something happens to their food source, they have a way of not starving to death until they find more algae to eat. "

This biological adaptation is also a mechanism of rapid evolution, Pierce says. "When a successful transfer of genes between species occurs, evolution can basically happen from one generation to the next," he notes, rather than over an evolutionary timescale of thousands of years.

Explore further: Solar-powered sea-slugs live like plants, prof says

More information: Schwartz JA, Curtis NE, and Pierce SK (2014) FISH labeling reveals a horizontally transferred algal (Vaucheria litorea) nuclear gene on a sea slug (Elysia chlorotica) chromosome. Biol. Bull. 227: 300-312. www.biolbull.org/content/227/3/300.full.pdf+html

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LariAnn
1 / 5 (3) Feb 03, 2015
I've known of this for years - it is not just the gene for maintaining the chloroplasts. If you've ever seen what this slug looks like before it "steals" the chloroplasts, you'd know that it is brown and looks just like a typical slug. Once it gets the chloroplasts online, it turns into the "crawling leaf" shown here. That morphological change to a leaf shape has to involve some genetic switching or extra genes, especially because the alga is not a plant that has leaves! I'd like to see some transgenic study - an attempt to get a land-based brown slug to become a crawling leaf slug like this one. Interesting stuff!
Whydening Gyre
4.6 / 5 (11) Feb 03, 2015
Wow... I guess that old "you are what you eat" adage is taking on a whole new meaning...
katesisco
1.8 / 5 (5) Feb 03, 2015
No way on Earth for this to happen yet it does.
FainAvis
not rated yet Feb 03, 2015
Snail says, "Oh, that is a neat bit of code, I think I will use that in my next generation‽" An interesting example of genetic open source code.
Did the leafy sea dragon do the same? Or the mantis knighted with orchid pollen?
Whydening Gyre
4.5 / 5 (8) Feb 03, 2015
The simpler the organism, the more adaptable to environment?
Sounds like the more specialized an organism becomes the more suscepteable to environmental change....
Whydening Gyre
4.5 / 5 (8) Feb 04, 2015
I've known of this for years - it is not just the gene for maintaining the chloroplasts. If you've ever seen what this slug looks like before it "steals" the chloroplasts, you'd know that it is brown and looks just like a typical slug. Once it gets the chloroplasts online, it turns into the "crawling leaf" shown here. That morphological change to a leaf shape has to involve some genetic switching or extra genes...

Wikipedia gives a little info on it, if you care to read...
The "shape change" is a matter of juvenile to adult growth.
Additionally -
"More recent analyses, however, were unable to identify any actively expressed algal nuclear genes in Elysia cholorotica, or in the similar species Elysia timida and Plankobranchus ocellatus. [9][10] These results weaken support for the horizontal gene transfer hypothesis.[10]
JVK
1 / 5 (5) Feb 04, 2015
See also from June 2012: http://mbe.oxford...abstract

"...symbiotic chloroplasts residing inside the host molluscan cell are maintained by an interaction of both organellar and host biochemistry directed by the presence of transferred genes."

More than 2 years ago they linked light-induced amino acid substitutions in plants to algae and to molluscs, which exemplifies how the sun's biological energy fuels the ever-increasing nutrient-dependent chemistry of life that links biophysically constrained protein folding to biodiversity.

The diversity of morphological and behavioral phenotypes is nutrient-dependent but it is also controlled by the metabolism of nutrients to species-specific pheromones. In species from microbes to man, pheromones control the physiology of reproduction, which enables population-wide fixation of beneficial amino acid substitutions.

There's a model for that:
http://www.ncbi.n...24693353
JVK
1 / 5 (5) Feb 04, 2015
The "shape change" is a matter of juvenile to adult growth.


This links the 3D to the 4D genome without the pseudoscientific nonsense about mutations and evolution.

It's why serious scientists have been trying to determine how conserved molecular mechanisms enable "...nucleome structure changes as cells age, differentiate, and divide..."

However, many researchers appear to believe in ridiculous theories. They think molecules automagically evolve in deep space and cosmic rays cause mutations to the cells that automagically formed from the molecules that arrived on earth via transport by asteroids or aliens.

Their theories about molecules to man evolution make no sense to those who understand the requirement for an atoms to ecosystems model of biologically-based cause and effect.

Theories convince the biologically uninformed who are not interested in learning anything about biological facts.
http://comments.s....6217.10
JVK
1 / 5 (5) Feb 04, 2015
I'd like to see some transgenic study - an attempt to get a land-based brown slug to become a crawling leaf slug like this one.


SICB (2015) inadvertently and unknowingly linked the conserved molecular mechanisms for changes in the morphology and behavior of crustaceans and insects without realizing that the sun's biological energy and nutrient-dependent amino acid substitutions differentiate all the cells in all the individuals of all species.

See: http://www.scienc...20.short

and my comment: http://comments.s...6219.220
cjn
5 / 5 (5) Feb 04, 2015
Gyre:[qWikipedia gives a little info on it, if you care to read...
The "shape change" is a matter of juvenile to adult growth.
Additionally -
"More recent analyses, however, were unable to identify any actively expressed algal nuclear genes in Elysia cholorotica, or in the similar species Elysia timida and Plankobranchus ocellatus. [9][10] These results weaken support for the horizontal gene transfer hypothesis.[10]
The important part was in the next bit:
"Genomic analysis of Acetabularia acetabulum and Vaucheria litorea, the primary food sources of Elysia timida, has revealed that their chloroplasts produce ftsH, another protein essential for photosystem II repair. In land plants, this gene is always encoded in the nucleus, but is present in the chloroplasts of most algae."

No need for HGT with these acting as self-sustained power plants. Its really remarkable when you think about it.
Moebius
5 / 5 (2) Feb 04, 2015
I used to look at my ponds water under a microscope when I was a kid. I once saw a green ping pong paddle shaped thing corkscrewing through the water. It was the color of chlorophyll and moved on its own. Never saw anything like it until now.
JVK
1 / 5 (3) Feb 04, 2015
Its really remarkable when you think about it.


Indeed. It makes me wonder why the biologically uninformed have attributed biologically-based cause and effect to mutations and evolution instead of to the epigenetic effects of the sun's biological energy on nutrient-dependent cell type differentiation controlled by the physiology of reproduction.

It's as if they never though about anything except mutations during decades of pseudoscientific nonsense that claimed they led to the evolution of increasing organismal complexity.
Ozmandias
5 / 5 (1) Feb 04, 2015
We need to start eating blind mole rats to get those anti-cancer genes.
Whydening Gyre
4.2 / 5 (5) Feb 04, 2015
Indeed. It makes me wonder why the biologically uninformed have attributed biologically-based cause and effect to mutations and evolution instead of to the epigenetic effects of the sun's biological energy on nutrient-dependent cell type differentiation controlled by the physiology of reproduction.

It's as if they never though about anything except mutations during decades of pseudoscientific nonsense that claimed they led to the evolution of increasing organismal complexity.

You are, of course referring to mutational "adaptation"... What the hell do you think organisms are adapting around/to ? Daft, Daft, Daft....
Get a thought process that means something...
JVK
1 / 5 (3) Feb 04, 2015
How Did the Code Of Life Pass Through Primitive Cells?
http://m.space.com/28448-origin-life-code-primitive-cells.html

A recent report links light-induced amino acid substitutions from plants to unicelluar algae and to a multicellular sea slug. "FISH Labeling Reveals a Horizontally Transferred Algal (Vaucheria litorea) Nuclear Gene on a Sea Slug (Elysia chlorotica) Chromosome" http://www.biolbu...abstract

That makes it easier to link microRNAs from crustaceans to insects via the conserved molecular mechanisms we detailed in 1996 that linked insects to mammals, including primates. Dobzhansky (1973) also linked amino acid substitutions to cell type differentiation. "...the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla." http://www.jstor..../4444260
JVK
1 / 5 (3) Feb 05, 2015
You are, of course referring to mutational "adaptation"


No, I obviously am not. Please explain how mutations that perturb protein folding lead to adaptation. Alternatively, stop claiming that they lead to anything except physiopathology, which is what all experimental evidence of biologically-based cause and effect clearly indicates.

What the hell do you think organisms are adapting around/to ?


Thanks for asking. Organisms adapt to ecological variation in their food supply. What else could they adapt to? How else could they adapt if their physiology of reproduction was not nutrient-dependent and pheromone-controlled?

Get a thought process that means something...


Thanks for the suggestion. You should consider buying a thought process from someone who has one for sale, since you will otherwise clearly remain without one of your own.
RealScience
5 / 5 (5) Feb 05, 2015
The biologically uninformed continue to yell: MUTATIONS! (JVK, DEC 18, 2014)


I'll let your own words do the talking, JVK, since you have YET AGAIN introduced that term to a thread. And you used it FOUR TIMES before anyone else did.

ROTFLMAO!
JVK
1 / 5 (3) Feb 05, 2015
you have YET AGAIN introduced that term to a thread.


You are not addressing the accuracy of my claims with any experimental evidence that supports a different model of cell type differentiation.

Not surprisingly, cell type differentiation appears to be nutrient-dependent and pheromone-controlled in all animal species based on the origins of feedback loops and chromatin loops that obviously are linked to cell type control of hydration, which requires control of membrane permeability to ions and amino acids.

Control is biophysically constrained by the RNA-mediated chemistry of protein folding, which links light-induced amino acid substitutions in plants and algae to animals via the sea slug.

I think science idiots are going to pretend that they never believed in the theories about mutations and evolution because the theories now seem as ridiculous to the biologically uninformed as they have always been known to be by serious scientists.
RealScience
5 / 5 (5) Feb 05, 2015
you have YET AGAIN introduced that term to a thread.


You are not addressing the accuracy of my claims with any experimental evidence that supports a different model of cell type differentiation.


Why would I address your claims or support a different model of cell type differentiation? Are you confusing cell type differentiation within an organism with long-term evolution of the the organisms descendents?

Cell type differentiation IS largely RNAs and epigenetics (although gene sequence changes such as transposons are known to play some role in neurons).

In contrast, you have been presented experimental evidence numerous times that mutations (DNA base pair sequence changes) occur and are sometimes selected for in evolution.

But you ADMIT that you throw such results out:

I can throw out results that appear to attest to mutations as the cause of adaptive evolution because no evidence suggests that is possible.

JVK
1 / 5 (3) Feb 05, 2015
https://books.goo...b5IDkSQC
At Home in the Universe: The Search for Laws of Self-organization and Complexity
Stuart A. Kauffman
1995

The Scent of Eros: Mysteries of Odor in Human Sexuality
http://www.amazon...9523383X
1995/2002

https://books.goo...lZ8vnVYC
Reinventing the Sacred: A New View of Science, Reason, and Religion
Stuart A. Kauffman
2010

https://books.goo...cdmhjIYC
Mind and Cosmos: Why the Materialist Neo-Darwinian Conception of Nature is Almost Certainly False
Thomas Nagel

Two of the books above predicted the findings in Nutrient-dependent/pheromone-controlled adaptive evolution: a model. http://www.ncbi.n...24693353

Those findings link light-induced amino acid substitutions to cell type differentiation in all cells of all individuals of all species from microbes to man.
JVK
1 / 5 (3) Feb 05, 2015
Cell type differentiation IS largely RNAs and epigenetics


What kind of science idiot reasserts the claim that I have made in a series of published works since 1995 and then adds:

you have been presented experimental evidence numerous times that mutations (DNA base pair sequence changes) occur and are sometimes selected for in evolution.


He might just as well claim to not know the difference between an amino acid substitution and a mutation.

See: Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors http://www.ncbi.n...24693349

Conclusion: Olfaction and odor receptors provide a clear evolutionary trail that can be followed from unicellular organisms to insects to humans (Keller et al., 2007; Kohl, 2007; Villarreal, 2009; Vosshall, Wong, & Axel, 2000)."

See for comparison: "...constraint-breaking mutation is the ultimate source of all biological innovations... Nei (2013)
Whydening Gyre
4.3 / 5 (6) Feb 05, 2015
Cell type differentiation IS largely RNAs and epigenetics


you have been presented experimental evidence numerous times that mutations (DNA base pair sequence changes) occur and are sometimes selected for in evolution.


He might just as well claim to not know the difference between an amino acid substitution and a mutation.


So... explain, exactly, what DOES cause amino acid substitutions...
RealScience
5 / 5 (7) Feb 05, 2015

What kind of science idiot...


You mean the one who yelled "mutations" into this thread?


This links the 3D to the 4D genome without the pseudoscientific nonsense about mutations ...

They think ... cosmic rays cause mutations...

... attributed biologically-based cause and effect to mutations ...

It's as if they never though about anything except mutations...

JVK, Feb 04, 2015


Goes perfectly with your statement:
The biologically uninformed continue to yell: MUTATIONS! (JVK, DEC 18, 2014)


LMAO again!
RealScience
5 / 5 (7) Feb 05, 2015
He might just as well claim to not know the difference between an amino acid substitution and a mutation.


I already explained to you the most common relationship between mutations and amino acid substitutions, JVK.

From http://phys.org/n...lei.html

@JVK - the archetypical mutation is a single nucleotide change in the DNA sequence of the coding portion of a gene. And what effect does this have? Looking at the 9 possible single changes for each of the 64 codons, 138 out of 576 are synonymous (no change to the protein sequence coded), 50 change to or from stop codons and change the length of the protein, and 388, or 67% CAUSE AN AMINO ACID SUBSTITUTION in the resulting protein

So if amino acid substitutions are selected because they stabilize proteins, so too are mutations that cause them.

Checkmate again, JVK!


Do you need it explained more clearly?
JVK
1 / 5 (4) Feb 05, 2015
Do you need it explained more clearly?


Yes. How does perturbed protein folding lead to fixation of an amino acid substitution? You seem to be trying to tell others

1) Here's a mutation
2) Here's an amino acid substitution
3) Obviously, the mutation caused the amino acid substitution.

Only a science idiot would think that's an explanation of biologically based cause and effect.
JVK
1 / 5 (4) Feb 05, 2015
So... explain, exactly, what DOES cause amino acid substitutions...


"Nutrient-dependent/pheromone-controlled adaptive evolution: a model" http://www.ncbi.n...24693353

The title of my last published review is a clear indicator that nutrient uptake causes the amino acid substitutions, and that the amino acid substitutions are fixed in the organized genomes of species from microbes to man via the pheromone-controlled physiology of reproduction. Cause and effect are linked across animal species via examples of how the epigenetic landscape becomes the physical landscape of DNA in species from microbes to man via the biophysically constrained chemistry of RNA-mediated protein folding that links feedback loops to chromatin loops and the biodiversity that science idiots attribute to mutations.
JVK
1 / 5 (4) Feb 05, 2015
(2013) Mention of mutations in
The Surprising Origins of Evolutionary Complexity
http://www.scient...plexity/
"...mutations arise, complexity emerges as a side effect, even without natural selection..."

(2015) No mention of mutations in the evolution of bedbugs
In Bedbugs, Scientists See a Model of Evolution
http://www.nytime...tml?_r=1

In the 2013 article, Zimmer wrote "Complexity, they say, is not purely the result of millions of years of fine-tuning through natural selection.... To some extent, it just happens."

Without natural selection, his claim amounts to this: Mutations cause evolution to "just happen."

What kind of biologically uninformed science journalist can't keep his claims straight and avoid repeatedly putting his foot in his mouth?

(2015) "The insects also evolved adaptations for feeding on human blood."

How?
RealScience
5 / 5 (7) Feb 05, 2015
Do you need it explained more clearly?


Yes. How does perturbed protein folding lead to fixation of an amino acid substitution? You seem to be trying to tell others

1) Here's a mutation
2) Here's an amino acid substitution
3) Obviously, the mutation caused the amino acid substitution.


OK, I would be happy to explain more clearly.

1) Ribosomes produce proteins by translating messenger RNAs (mRNAs) into the sequences of amino acids that form the protein.

The mRNAs are likely to be extensively edited in this process before they get to the ribosome, such as by removing introns and splicing together the remaining exons, but MOST of the amino acids in most proteins are specified in the sequences of RNA bases in exons of the messenger RNA.

Do you agree so far?
RealScience
5 / 5 (7) Feb 05, 2015
In the 2013 article, Zimmer wrote "Complexity, they say, is not purely the result of millions of years of fine-tuning through natural selection.... To some extent, it just happens."

Without natural selection, his claim amounts to this: Mutations cause evolution to "just happen."


Um, JVK, the Zimmer quote does not say that evolution happens entirely without natural selection.

Did you miss the "not purely" and "some extent"? Let me highlight them for you:

"Complexity, they say, is NOT PURELY the result of millions of years of fine-tuning through natural selection.... To SOME EXTENT, it just happens."
JVK
1.8 / 5 (5) Feb 05, 2015
Do you agree so far?


I agree that you are a science idiot. Nothing more. You seem to know nothing about the thermodynamic cycles of protein biosynthesis and degradation that I have detailed, and are going to keep trying to tell me about cell type differentiation via mutations.

Nutrient-dependent / Pheromone-controlled adaptive evolution: (a mammalian model of thermodynamics and organism-level thermoregulation) http://youtu.be/DbH_Rj9U524
RealScience
5 / 5 (7) Feb 06, 2015
Do you agree so far?

You seem to know nothing about the thermodynamic cycles of protein biosynthesis and degradation that I have detailed, and are going to keep trying to tell me about cell type differentiation via mutations.


JVK, I have already pointed out that in contrast to long-term evolution of an organism's descendants, cell type differentiation happens within an organism (and that is largely RNAs and epigenetics). YOU are the one who keeps confusing cell type differentiation with evolution.

As for protein biosynthesis, I outlined a clearly defined step in the commonly-accepted process of protein biosynthesis and asked whether you agreed with it. This is relevant because protein synthesis is PART of the most common relationship between mutations and amino acid substitutions, which you said that you need explained to you more clearly.

I will ask again and separate whether you understand from whether you agree:

- continued -
RealScience
5 / 5 (6) Feb 06, 2015
- continued -

1) Ribosomes produce proteins by translating messenger RNAs (mRNAs) into the sequences of amino acids that form the proteins.

The mRNAs are likely to be extensively edited in this process before they get to the ribosome, such as by removing introns and splicing together the remaining exons, but MOST of the amino acids in most proteins are specified in the sequences of RNA bases in exons of the messenger RNA.

Do you agree that this is PART of the way in which most proteins are synthesized?

If you do NOT agree with this, please state which part you disagree with.

If you do NOT understand this, please state which part you do not understand and I will explain that part in more detail.

(Note that this is just one of several steps the explanation of the most common relationship between mutations and amino acid substitutions).
Whydening Gyre
4.2 / 5 (5) Feb 06, 2015
...The title of my last published review is a clear indicator that nutrient uptake causes the amino acid substitutions...

could it be that disruptions of nutrient uptake cause impaired or erroneous substitutions? Some of which are lucky enough to epigenetically survive thru reproduction?
Subsequently resulting in "mutations'?
And a few of those being beneficial and surviving further?
Mutation means change (via naturally evolving mechanics in any particular species), not an end.
Whydening Gyre
4.3 / 5 (6) Feb 06, 2015
Dang it.. gotta ease up on the coffee...
accidentally hit 5 star for cole, while I was 5ing all of RS's comments...
Whydening Gyre
4.2 / 5 (5) Feb 06, 2015
could it be that disruptions of nutrient uptake cause impaired or erroneous substitutions? Some of which are lucky enough to epigenetically survive thru reproduction?
Subsequently resulting in "mutations'?
And a few of those being beneficial and surviving further?

Lest I forget - what about uptake of nutrients that the were not on the organism's usual menu?
RealScience
5 / 5 (5) Feb 06, 2015
could it be that disruptions of nutrient uptake cause impaired or erroneous substitutions? Some of which are lucky enough to epigenetically survive thru reproduction?
Subsequently resulting in "mutations'?
And a few of those being beneficial and surviving further?

Lest I forget - what about uptake of nutrients that the were not on the organism's usual menu?


@WG - there is some evidence that genes that are used more are more likely to mutate, so if cells start to use an unusual gene to process a new nutrient then that gene may be more likely mutate.
Since cells have been shown to share RNAs (which can turn on genes), this could indirectly affect gene copies in germ-line cells. Some such mutations would be detrimental, while others, such as an increase in copy numbers or an added promoter, would be useful if the new nutrient becomes common.

Regarding your older question, nutrient shortages are well known to increase mutation rates.
Whydening Gyre
4.3 / 5 (6) Feb 06, 2015
Lest I forget - what about uptake of nutrients that the were not on the organism's usual menu?


@WG - there is some evidence that genes that are used more are more likely to mutate, so if cells start to use an unusual gene to process a new nutrient then that gene may be more likely mutate.
Since cells have been shown to share RNAs (which can turn on genes), this could indirectly affect gene copies in germ-line cells. Some such mutations would be detrimental, while others, such as an increase in copy numbers or an added promoter, would be useful if the new nutrient becomes common.

Regarding your older question, nutrient shortages are well known to increase mutation rates.

Thanks, RS. Excellent input. I (kinda) rest my case...
Whydening Gyre
3 / 5 (2) Feb 06, 2015
Organisms adapt to ecological variation in their food supply. What else could they adapt to?

SIMPLER organisms do that.
How else could they adapt if their physiology of reproduction was not nutrient-dependent and pheromone-controlled?

A conscious decision of some sort. The ability of which is available at some pre-calculated level of complexity. It's all about the "critical mass"...
You tend to think we are the end of all this, but we are really just the middle of something else...
viko_mx
1 / 5 (4) Feb 07, 2015
Organisms have built in mechanisms for rapid adaptation to the possible light changes in the environment where they live in order to maintain harmonious relations and organic balance in nature. But different organisms to exchange genes is too bold claim. The same like people to borrow genes from vegetables they eat. I imagine a sworn carrots eater how will look his nose after some time. May be like Pinokio.
JVK
1 / 5 (4) Feb 07, 2015
The display of ignorance by biologically uniformed science idiots is exemplary. They collectively show it is useless to pursue a knowledge of physics, chemistry, and molecular biology and integrate the knowledge into a series of published works during the past two decades.

Anonymous fools will come here for information, instead. They will accept only the explanations of science idiots and never learn any facts about the biological basis of cell type differentiation that links DNA uptake, RNA-directed DNA methylation and RNA-mediated amino acid substitutions to the morphological and behavioral phenotypes of species from microbes to man via the conserved molecular mechanisms we detailed in the molecular genetics section of our 1996 Hormones and Behavior review.

From Fertilization to Adult Sexual Behavior http://www.hawaii...ion.html

-- extended in http://www.ncbi.n...24693353
JVK
1 / 5 (4) Feb 07, 2015
different organisms to exchange genes is too bold claim.


It's not a claim. It's a statement of fact based on results of experiments performed during the past 15 years by Sidney Pierce and others.

FISH Labeling Reveals a Horizontally Transferred Algal (Vaucheria litorea) Nuclear Gene on a Sea Slug (Elysia chlorotica) Chromosome http://www.biolbu...abstract

The experimental evidence supports all my claims, and all the claims of others who understand the biological basis for symbiosis across all species.

"...DNA uptake (Palchevskiy & Finkel, 2009) appears to have epigenetically 'fed' interspecies methylation and speciation via conjugation (Fall et al., 2007; Finkel & Kolter, 2001; Friso & Choi, 2002). This indicates that reproduction began with an active nutrient uptake mechanism in heterospecifics and that the mechanism evolved to become symbiogenesis in the conspecifics of asexual organisms (Margulis, 1998)."
Returners
1 / 5 (2) Feb 07, 2015
Horizontal gene transfer is not an example of the classic "evolution" taught in text books.
This is an existing trait/gene being used in another organism.

Classic "Evolution" is the hypothesis that all-new genes spontaneously appear on their own as adaptations to new environments.

This particular adaptation runs the risk of ending the organism's future adaptations anyway, because the ability to simply survive by acting like a plant or algae means it will no longer be selected as heavily for starvation.

I could see applications in food production and medicine production, but I am extremely wary of cross-species engineering, and especially cross-genus and cross-kingdom engineering.

I was thinking something like Fish farms and how it might be useful for them to be photosynthetic to grow with less cost to the farmers.
JVK
1 / 5 (2) Feb 07, 2015
Classic "Evolution" is the hypothesis that all-new genes spontaneously appear on their own as adaptations to new environments.


You forgot about the claim that de novo gene creation exemplifies the role of mutations in neo-Darwinism. This takes us back to Darwin's 'conditions of life.' They are obviously nutrient dependent and so are amino acid substitutions that differentiate the cell types of all individuals of all species.

If Dobzhansky had known how horizontal gene transfer occurred he would not have attributed evolution to mutations. He was a serious scientist who was decades ahead of his time .

See: Nothing in Biology Makes Any Sense Except in the Light of Evolution. "... the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla." Obviously, he meant the light of the sun but could only place the sun's energy into the context of mutations.
rich_aquilina
not rated yet Feb 08, 2015
Yes, yes, yes.... but can I steal their magic and make it my own by ingesting enough of them?
JVK
1 / 5 (2) Feb 08, 2015
Classic "Evolution" is the hypothesis that all-new genes spontaneously appear on their own as adaptations to new environments.


This is one of the most interesting claims that I have ever seen. Can anyone confirm that they believe in it, or provide a citation to support the claim? I'm concerned that science idiots may not know anything more about genesis and epistasis across species than to insist that metabolic networks and genetic networks are linked by the spontaneous appearance of all-new genes.

See for instance: Mutation-Driven Evolution http://www.amazon...99661731
"...genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world. In this view of evolution there is no need of considering teleological elements."

Does that mean
1) All-new genes spontaneously appear
2) Mutate
and
3) lead to all the biodiversity in the world?
JVK
1 / 5 (2) Feb 08, 2015
I already explained to you the most common relationship between mutations and amino acid substitutions, JVK.


Please explain it in terms like this:
Classic "Evolution" is the hypothesis that all-new genes spontaneously appear on their own as adaptations to new environments.


Do you think that mutations cause all-new genes to spontaneously appear?

Alternatively, please explain it in terms that might make sense to an intelligent person.

Whydening Gyre
4 / 5 (4) Feb 08, 2015
Do you think that mutations cause all-new genes to spontaneously appear?

Not spontaneous. a result of subsequent "additions" over numerous generations. The universes way to weed out the beneficial from the non-beneficial (via natural selection)
It's just 1+1 = a new one.
(Which the Universe considers just another 1, so it attempts to add that to something else.)

Alternatively, please explain it in terms that might make sense to an intelligent person.

If you can't get something that simple, then guess what...?


RealScience
5 / 5 (3) Feb 08, 2015
Alternatively, please explain it in terms that might make sense to an intelligent person.

OK, since you haven't disagreed with MOST of the amino acids in most proteins being specified in the sequences of RNA bases in exons of the messenger RNA, I will continue explaining clearly to you the most common relationship between mutations and amino acid substitutions.

The messenger RNAs are produced by RNA polymerase, which transcribes the sequence of base pairs in a gene into an RNA version thereof. So the sequence of the DNA base pairs in the DNA gene determines the sequence of bases in the messenger RNA.

Do you agree that this is PART of the way in which most proteins are synthesized?

If you do NOT agree with this, please state which part you disagree with.

If you do NOT understand this, please state which part you do not understand and I will explain that part in more detail.
JVK
1 / 5 (2) Feb 08, 2015
The messenger RNAs are produced by RNA polymerase, which transcribes the sequence of base pairs in a gene into an RNA version thereof. So the sequence of the DNA base pairs in the DNA gene determines the sequence of bases in the messenger RNA.

Do you agree that this is PART of the way in which most proteins are synthesized?


Of course I do not agree. There is no model of biologically based protein biosynthesesis and degradation that suggests it begins with RNA polymerase and messenger RNAs. Your concept of how DNA base pairs cause changes in messenger RNA that somehow link the epigenetic landscape to the physical landscape of DNA in the organized genomes of microbes to man is more ridiculous than that claim by "Returners"

...that all-new genes spontaneously appear on their own as adaptations to new environments.


or the claim by Nei (2013) constraint-breaking mutation is the ultimate source of ... the enormous amount of biodiversity."
JVK
1 / 5 (2) Feb 08, 2015
If you can't get something that simple, then guess what...?


Thanks for asking. The answer is obvious. Only simple-minded biologically uninformed science idiot would accept such utter nonsense as if it had any explanatory power in the context of physics, chemistry, or molecular biology.

The universes way to weed out the beneficial from the non-beneficial (via natural selection)
It's just 1+1 = a new one.


Is there a model for that?

Whydening Gyre
4 / 5 (4) Feb 08, 2015
If you can't get something that simple, then guess what...?


Thanks for asking. The answer is obvious. Only simple-minded biologically uninformed science idiot would accept such utter nonsense as if it had any explanatory power in the context of physics, chemistry, or molecular biology.

The universes way to weed out the beneficial from the non-beneficial (via natural selection)
It's just 1+1 = a new one.


Is there a model for that?


WE are it...
RealScience
5 / 5 (2) Feb 08, 2015
@JVK, you claim:
There is no model of biologically based protein biosynthesesis and degradation that suggests it begins with RNA polymerase and messenger RNAs.


Great! So links to a model of biologically based protein biosynthesesis that suggests it begins with RNA polymerase and messenger RNAs will clearly show that this statement of yours is wrong.

http://www.nature...tein-393

So do you admit that there is a model for it?
JVK
1 / 5 (3) Feb 08, 2015
Only the biologically uninformed think Clancy is describing a model of cause and effect. For example, elsewhere she claims:

"Beta hemoglobin (beta globin) is a single chain of 147 amino acids. As previously mentioned, in sickle-cell anemia, the gene for beta globin is mutated."

That's the pseudoscientific nonsense that Denis Noble addressed when he wrote: "If you learnt evolutionary biology and genetics a decade or more ago you need to be aware that those debates have moved on very considerably, as has the experimental and field work on which they are based. (p 1014)" http://jp.physoc....007.full

It's also what Dobzhansky (1973) addressed when he wrote: "...the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla."

Anyone who places amino acid substitutions and differences in hemoglobin into the context of evolution is a science idiot.
anonymous_9001
5 / 5 (3) Feb 09, 2015
Clancy is describing the sequence of events that occurs between DNA, mRNA, and protein.

You have an odd definition of model and you attach an odd significance to it. We know very well how transcription and translation work at the molecular level. What does a "model" add to that? The two recognized uses of "model" in the biological sciences are model organisms and mathematical models.
JVK
1 / 5 (2) Feb 09, 2015
The two recognized uses of "model" in the biological sciences are model organisms and mathematical models.


The honeybee model organism links physics, chemistry, and communication to life. Clancy may have been taught, like you, to meaningfully interpret results from mutagenesis experiments as if they could epigenetically link the sun's biological energy to the diversity of morphological and behavioral phenotypes.

She has helped to teach others, like you, to become biologically uninformed science idiots. You provided an example of that fact in

Criticisms of the nutrient-dependent pheromone-controlled evolutionary model. http://www.ncbi.n...24959329

Nutrient-dependent/pheromone-controlled adaptive evolution: a model. http://www.ncbi.n...24693353

Now that others know your criticisms were based on your mutagenesis experiments, they can dismiss anything you say and everything Clancy and others have said about cell type differentiation.
JVK
1 / 5 (2) Feb 09, 2015
Re:
Anyone who places amino acid substitutions and differences in hemoglobin into the context of evolution is a science idiot.


All of the different types of channels have basically the same five amino acid sequences in the selectivity filter.

http://jonlieffmd...channels

In my model of epigenesis and epistasis, the cell types of all cells in all individuals of all species are differentiated by light-induced amino acid substitutions that link ecological variation to ecological adaptation via biophysically constrained feedback loops and the chemistry of chromatin loops linked to RNA-mediated protein folding. See for comparison: Jones, Andrew "Lipid Encapsulation of Self Replicating Ribozymes" http://www.scribd...s#scribd

Ask Jones (aka anonymous_9001) how much it costs to become a science idiot. He is a model of ignorance.
JVK
1 / 5 (2) Feb 09, 2015
Excerpt from Jones http://www.scribd...s#scribd

"The evolution of a successful RNA polymerase ribozyme is a lofty goal. While its discovery would not be the be-all and end-all of abiogenesis research, it would represent an important stepping stone between prebiotic chemistry and life. The encapsulation of such a ribozyme is also an important step, as it would enable a system of heredity and evolution through natural selection. Based on progress in current research, it is only a matter of time before that ribozyme is discovered."

See for comparison: A quantum theory for the irreplaceable role of docosahexaenoic acid in neural cell signalling throughout evolution http://www.ncbi.n...23206328

Ask Jones how physics and chemistry and information are linked to abiogenesis in his thesis.
RealScience
5 / 5 (3) Feb 09, 2015
Only the biologically uninformed think Clancy is describing a model of cause and effect. For example, elsewhere she claims...


What does what Clancy claims elsewhere have to do with whether she is describing a model in the NatureEducation article?

Only someone who is blind to anything that disagrees with him would deny that what Clancy describes is a model of biologically based protein synthesis. It is a model that has been elucidated at the molecular level, and key parts of the model have won Nobel prizes.

You might DISAGREE with the model, but to deny that it exists is both morally and intellectually DISHONEST.

RealScience
5 / 5 (2) Feb 09, 2015
The messenger RNAs are produced by RNA polymerase, which transcribes the sequence of base pairs in a gene into an RNA version thereof. So the sequence of the DNA base pairs in the DNA gene determines the sequence of bases in the messenger RNA.

Do you agree that this is PART of the way in which most proteins are synthesized?

Of course I do not agree.


So which part do you disagree with?

Do you disagree that DNA contains genes whose sequence of DNA base pairs gets transcribed into RNA bases?
Do you disagree the sequence of RNA bases depends in part on the sequence of DNA bases in the gene?

(Note that I am not asking whether this is the complete process or that all proteins are made this way, but whether you agree that this is PART of the process in which most proteins are made.)
Do you disagree that RNAare produced by transcribing
JVK
1 / 5 (2) Feb 09, 2015
...what Clancy describes is a model of biologically based protein synthesis.


What you call a model is a ridiculous theory that is not linked to protein degradation by feedback loops that typically eliminate most mutations. The ridiculous theory can be compared via examples from my model of RNA-mediated amino acid substitutions that stabilize DNA in the organized genomes of species from microbes to man.

Stop asking me questions based on your ignorance of biologically-based cause and effect, and learn what Nobel Laureate Linda Buck is talking about in the paper she co-authored:
Feedback loops link odor and pheromone signaling with reproduction http://www.scienc...05009815

Although other science idiots may not see what you are trying to do, serious scientists recognize that you are trying to pick apart a model and compare it to a ridiculous theory to make the ridiculous theory seem to be more believable than the model.
anonymous_9001
4.7 / 5 (3) Feb 09, 2015
Stop asking me questions based on your ignorance of biologically-based cause and effect


Asking if you understand the transcription-translation process is a question based on YOUR ignorance because you seem to not know that amino acids are determined by codons in the DNA.

protein degradation by feedback loops that typically eliminate most mutations


What is this supposed to mean? Proteins break down and cause mutations to be eliminated? How?
RealScience
5 / 5 (2) Feb 09, 2015
What you call a model is a ridiculous theory that is not linked to protein degradation by feedback loops that typically eliminate most mutations...

Stop asking me questions based on your ignorance...


You asked for a clearer explanation of the most common way that mutations cause amino acid substitutions, so I am providing that.

The question that I am ask are based on YOUR ignorance.

We can next discuss amino acid substitutions causing SOME proteins to misfold and be degraded by feedback loops, if you need that explained to you as well.

learn what Nobel Laureate Linda Buck is talking about in the paper she co-authored


Are you claiming that the 'feedback loops' paper you linked is relevant to whether DNA genes are transcribed to messenger RNAs that are (after editing) translating into proteins?

And are you claiming that we should accept that the paper is valid because on of the authors got a Nobel prize?
RealScience
5 / 5 (3) Feb 10, 2015
JVK, YOU are the one who should learn from the "feedback loops" paper that you linked.

Supporting pheromones having effects in mammals does NOT make the paper evidence against proteins being translated from mRNA that is transcribed from DNA genes.

In contrast, the paper's experiment DEPENDS ON the translation of DNA genes into mRNAs and thence into protein. This is shown in Figure 1A and its description:
In the BIG transgene, the promoter of the mouse GnrhL gene is fused to a BL coding region, an IRES, and a GFP coding sequence. The IRES permits independent translation of BL and GFP proteins from the resulting bicistronic mRNA.


Since you are comprehension-challenged, I'll pick out key words for you:
... gene ... coding sequence ... translation of ... proteins from ... mRNA.


So the Nobel Laureate's paper that you linked DEPENDS ON what you just called "a ridiculous theory" that you "do not agree" with.

Checkmate again, JVK!
JVK
1 / 5 (2) Feb 10, 2015
A symbiotic liaison between the genetic and epigenetic code http://journal.fr...113/full
Excerpt: "...the model is further extendable to virtually all traceable molecular traits."

"The association of [RNA-directed] DNA methylation and [RNA-mediated amino acid substitutions with the] genetic sequence displays an exemplary application, which is further extendable to virtually all traceable cellular features, including proteomics or metabolomics, among many others. It will be the knowledge of these complex relationships that will drive future efforts to resolve the conundrum of human variation in physiological and pathological contexts."

It will be biologically uninformed science idiots who are responsible for others efforts, like those who are Combating Evolution to Fight Disease http://www.scienc...88.short
Whydening Gyre
3 / 5 (2) Feb 11, 2015
Although other science idiots may not see what you are trying to do, serious scientists recognize that you are trying to pick apart a model and compare it to a ridiculous theory to make the ridiculous theory seem to be more believable than the model.

The thing with models is... they're still just a theory...
Vietvet
1.8 / 5 (5) Feb 11, 2015
@Wydening Gyre
If jvk's model had any merit he wouldn't need to so desperately trying to sell it.
No one is buying it.
JVK
1 / 5 (2) Feb 11, 2015
If jvk's model had any merit he wouldn't need to so desperately trying to sell it.
No one is buying it.


It's not something that you buy; it's an explanation of biologically-based cause and effect that you accept or not. If not, you can continue to believe in pseudoscientific nonsense.

That's what most people prefer to do because they are biologically uninformed science idiots who claim:

The thing with models is... they're still just a theory...


See for comparison: Light- and Carbon-Signaling Pathways. Modeling Circuits of Interactions http://www.plantp...abstract
RealScience
5 / 5 (2) Feb 11, 2015
A symbiotic liaison between the genetic and epigenetic code

Exactly - both the genetic and AND epigenetic codes play a role.

To continue with how mutations in DNA can cause amino acid substitutions, the genetic code uses a 3-DNA-base "codon" to specify each amino acid in a protein.

The archetypical 'point' mutation changes one bases in one codon of a gene. With 4 DNA bases in the genetic code, each of a codon's bases could be changed into 3 different bases, and there are 4*4*4 = 64 possible codons so there 3*3*64 = 576 different possible point mutations.

Most amino acids have several codons, and 138 of these mutations don't change the amino acid being coded for. Also 50 changes are to or from a STOP codon.

But the other 388 out of 576 cause one amino acid to be substituted for another in the resulting protein. So that, JVK, is how 67% of possible point mutations in a gene cause an amino acid substitution in the resulting protein.
JVK
1 / 5 (2) Feb 12, 2015
African Glucose-6-Phosphate Dehydrogenase Alleles Associated with Protection from Severe Malaria in Heterozygous Females in Tanzania http://dx.doi.org....1004960

Everything known about ecological variation that led to ecological adaptations manifested in nutrient-dependent pheromone-controlled sex differences in cell types was linked to the advent of sexual reproduction in yeasts in our 1996 Hormones and Behavior review: From Fertilization to Adult Sexual Behavior http://www.hawaii...ion.html

Everything touted by theorists in the context of mutations and evolution has continued to contribute to millions of deaths and much more suffering than most people can imagine.

Yet, here we find the science idiots who are literally killing people with ignorance, while others are "Combating Evolution to Fight Disease" http://www.scienc...88.short
RealScience
5 / 5 (3) Feb 12, 2015
Yet again I have to explain your own citation to you, JVK. Rather than being a refutation, your "... Alleles Associated with Protection from Severe Malaria ..." citation is an EXAMPLE of point mutations causing amino acid substitutions in proteins.

The study

identified 68 G6PD polymorphisms and analysed 29 of these
...
Many of these known genetic variants result in amino acid changes and have been detected through sequencing the G6PD gene


Table 2 shows WHICH base in the DNA sequence for the gene is changed, and what it has changed to.

DNA sequence changes match the stqandard definition of 'mutations', and that the authors consider these 'mutations' can be seen from the text following Table 2:
... haplotype 1 = GGGAGTC, 2 = AACGGCT (6 mutations), 3 = AACGACT (7 mutations), 4 = AGGGGCC (3 mutations)). Female controls had a higher frequency of the three haplotypes (2–4) containing mutations ...


- continued -
RealScience
5 / 5 (3) Feb 12, 2015

- continued -

Furthermore this citation also contains an example of DESTABILZING a protein being beneficial, and of beneficial mutations being selected FOR.


It has been shown that coexistence of the two mutations is responsible for enzyme deficiency in G6PD A- because they act synergistically in causing instability of the enzyme.
...
This result shows that haplotypes with the 376G mutation have similar protective effect in heterozygotes irrespective of the presence or absence of the 202A mutation, indicating that the 376G mutation is causal.
...
We found that only females with one normal and one mutant copy of the gene (heterozygotes) were protected from severe malaria. Further, we established that the G6PD gene is under evolutionary pressure with the likely mechanism being selection by malaria.


Do you even read the articles that you cite, JVK, or is it that you fail to UNDERSTAND them?
anonymous_9001
5 / 5 (3) Feb 12, 2015
Another checkmate from RealScience.

Do you even read the articles that you cite, JVK, or is it that you fail to UNDERSTAND them?


A little of both from what I gather. And he still can't distinguish between expression and sequence.

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